In MATLAB 2015a online documentation for GO enrichment, i.e. "gene ontology enrichment in microarray data", there is an error in the sub-section titled "Looking at Probability of Gene Ontology Annotation".
In that sub-section, the hypergeometric PDF (hygepdf) is used to calculate p-values. The text says that this gives a "p-value": "This function returns the p-value associated to each term"
Probability density functions do not give a p-value.
The text should say "hygecdf" to get the hypergeometric cumulative distribution function (CDF). That will give a one-sided p-value to test under-representation. Though this tutorial probably wants the upper-tail to get the over-representation p-value, i.e. "hygepdf(..., 'upper')"